Several of instances involving Jeremy, like a running gag involving him trying to make a love nest out of yarn.
Not to mention his disastrous attempts to babysit. Poor guy...
Martin and Auntie Shrew exchanging insults. Funny because Martin is just a child.
While for the most part, the sequel was really awful, having Eric Idle voice Evil!Martin was awesome! He even had his own song! Wicked! It was the directors saving throw.
Brisby herself has funny moments. Pretty much saying no to Timmy wanting to go outside when he's whining about being in bed sick.
Mrs. Brisby flirting with Jeremy to convince him to watch her children!
Most of Brisby's scenes with Jeremy, just for how clearly he's getting on her nerves.
A bit of Black Comedy would be Mrs. Brisby's nervous laughter as she tries in vain to politely talk to Brutus as he's attempting to kill her!
The small moment of Snark-to-Snark Combat between Justin and Jenner when the former walks into the meeting hall with Mrs. Brisby and Mr. Ages.
Jenner: Hear me! The Thorn Valley Plan is the aspiration of idiots and dreamers. We [notices the trio and starts chuckling]...we were just talking about you. Justin: That's refreshing, Jenner. Usually you're screaming about us.